{"id":"https://openalex.org/W2138756513","doi":"https://doi.org/10.1093/bioinformatics/btp624","title":"Quantifying uncertainty in genotype calls","display_name":"Quantifying uncertainty in genotype calls","publication_year":2009,"publication_date":"2009-11-11","ids":{"openalex":"https://openalex.org/W2138756513","doi":"https://doi.org/10.1093/bioinformatics/btp624","mag":"2138756513","pmid":"https://pubmed.ncbi.nlm.nih.gov/19906825"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/2/242/48856326/bioinformatics_26_2_242.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/2/242/48856326/bioinformatics_26_2_242.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014248896","display_name":"Benilton S. Carvalho","orcid":"https://orcid.org/0000-0001-5122-5646"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benilton S. Carvalho","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005349228","display_name":"Thomas A. Louis","orcid":"https://orcid.org/0000-0002-3592-6386"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas A. Louis","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054612687","display_name":"Rafael A. Irizarry","orcid":"https://orcid.org/0000-0002-3944-4309"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rafael A. Irizarry","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA#TAB#","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014248896"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2353,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.92513673,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"26","issue":"2","first_page":"242","last_page":"249"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9555000066757202,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9470000267028809,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.6552483439445496},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49278882145881653},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.36913228034973145},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.33924999833106995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2923569083213806},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2639824450016022},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22174856066703796},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07661318778991699}],"concepts":[{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.6552483439445496},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49278882145881653},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.36913228034973145},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.33924999833106995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2923569083213806},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2639824450016022},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22174856066703796},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07661318778991699}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/2/242/48856326/bioinformatics_26_2_242.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19906825","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19906825","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2804295","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2804295","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:biostats.bepress.com:jhubiostat-1180","is_oa":false,"landing_page_url":"https://biostats.bepress.com/jhubiostat/paper180","pdf_url":null,"source":{"id":"https://openalex.org/S4377196124","display_name":"Collection of Biostatistics Research Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Johns Hopkins University, Dept. of Biostatistics Working Papers","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/2/242/48856326/bioinformatics_26_2_242.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309515","display_name":"George Washington University","ror":"https://ror.org/00y4zzh67"},{"id":"https://openalex.org/F4320310143","display_name":"Joslin Diabetes Center","ror":"https://ror.org/0280a3n32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138756513.pdf","grobid_xml":"https://content.openalex.org/works/W2138756513.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1566333899","https://openalex.org/W1708068686","https://openalex.org/W1973614663","https://openalex.org/W1978539871","https://openalex.org/W1978673080","https://openalex.org/W1993507262","https://openalex.org/W2003576629","https://openalex.org/W2038437697","https://openalex.org/W2058401000","https://openalex.org/W2066874799","https://openalex.org/W2081098333","https://openalex.org/W2093870110","https://openalex.org/W2097812771","https://openalex.org/W2101510083","https://openalex.org/W2115521447","https://openalex.org/W2134783591","https://openalex.org/W2140968934","https://openalex.org/W2141365440","https://openalex.org/W2149791927","https://openalex.org/W2155037683","https://openalex.org/W2162199336","https://openalex.org/W2170989872"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2134373856","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genome-wide":[1],"association":[2,78],"studies":[3],"(GWAS)":[4],"are":[5,43,98,191,292],"used":[6,73,183],"to":[7,76,151],"discover":[8],"genes":[9],"underlying":[10],"complex,":[11],"heritable":[12],"disorders":[13],"for":[14,69,113,153,196,217],"which":[15],"less":[16],"powerful":[17],"study":[18],"designs":[19],"have":[20,110,137],"failed":[21],"in":[22,35,50,124,272,283],"the":[23,39,44,70,92,141,161,167,180,202,212,231,240,250,257,269,284],"past.":[24],"The":[25,66,208,246],"number":[26],"of":[27,48,56,143,156,163,179,205,214,222,249,259,268],"GWAS":[28,51,75],"has":[29],"skyrocketed":[30],"recently":[31],"with":[32],"findings":[33,164],"reported":[34,165],"top":[36],"journals":[37],"and":[38,81,133,200,220,239,263,279],"mainstream":[40],"media.":[41],"Microarrays":[42],"genotype":[45,85,118,144],"calling":[46],"technology":[47],"choice":[49],"as":[52,277],"they":[53],"permit":[54],"exploration":[55],"more":[57],"than":[58],"a":[59,172],"million":[60],"single":[61],"nucleotide":[62],"polymorphisms":[63],"(SNPs)":[64],"simultaneously.":[65],"starting":[67],"point":[68],"statistical":[71,108],"analyses":[72],"by":[74,147,166,184,243],"determine":[77],"between":[79],"loci":[80],"disease":[82],"is":[83,253,275],"making":[84],"calls":[86,145],"(AA,":[87],"AB":[88],"or":[89],"BB).":[90],"However,":[91],"raw":[93,115],"data,":[94],"microarray":[95,125],"probe":[96],"intensities,":[97],"heavily":[99],"processed":[100],"before":[101],"arriving":[102],"at":[103,294],"these":[104,154],"calls.":[105,119],"Various":[106],"sophisticated":[107],"procedures":[109],"been":[111],"proposed":[112],"transforming":[114],"data":[116,291],"into":[117],"We":[120,170],"find":[121],"that":[122,192,230,254],"variability":[123,157,197],"output":[126],"quality":[127,162,215],"across":[128,198],"different":[129,131,134],"SNPs,":[130,218,261],"arrays":[132],"sample":[135],"batches":[136,199,221],"substantial":[138],"influence":[139],"on":[140,175],"accuracy":[142],"made":[146],"existing":[148],"algorithms.":[149],"Failure":[150],"account":[152,195],"sources":[155],"can":[158],"adversely":[159],"affect":[160],"GWAS.":[168],"RESULTS:":[169],"developed":[171],"method":[173,270],"based":[174],"an":[176],"enhanced":[177],"version":[178,186,233,237],"multi-level":[181],"model":[182,210],"CRLMM":[185,232,236],"1.":[187],"Two":[188],"key":[189],"differences":[190],"we":[193,228],"now":[194],"improve":[201],"call-specific":[203],"assessment":[204],"each":[206],"call.":[207],"new":[209,251],"permits":[211],"development":[213],"metrics":[216],"samples":[219,262],"samples.":[223],"Using":[224],"three":[225],"independent":[226],"datasets,":[227],"demonstrate":[229],"2":[234],"outperforms":[235],"1":[238],"algorithm":[241],"provided":[242],"Affymetrix,":[244],"Birdseed.":[245],"main":[247],"advantage":[248],"approach":[252],"it":[255],"enables":[256],"identification":[258],"low-quality":[260],"batches.":[264],"AVAILABILITY:":[265],"Software":[266],"implementing":[267],"described":[271],"this":[273],"article":[274],"available":[276,293],"free":[278],"open":[280],"source":[281],"code":[282],"crlmm":[285],"R/BioConductor":[286],"package.":[287],"SUPPLEMENTARY":[288],"INFORMATION:":[289],"Supplementary":[290],"Bioinformatics":[295],"online.":[296]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}